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Search results for: folded proteins
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Epitope Mapping of BmpA and BBK32 Borrelia burgdorferi Sensu Stricto Antigens for the Design of Chimeric Proteins with Potential Diagnostic Value
PublicationLyme disease is a tick-borne zoonosis caused by Gramnegative bacteria belonging to the Borrelia burgdorferi sensu lato (s.l.) group. In this study, IgM- and IgG-specific linear epitopes of two B. burgdorferi sensu stricto (s.s.) antigens BmpA and BBK32 were mapped using a polypeptide array. Subsequently, two chimeric proteins BmpABBK32-M and BmpA-BBK32-G were designed to validate the construction of chimeras using the identified...
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
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Patients with obstructive sleep apnea present with chronic upregulation of serum HIF-1α protein
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Unusual dynamic properties of water near the ice-binding plane of hyperactive antifreeze protein
PublicationThe dynamical properties of solvation water of hyperactive antifreeze protein from Choristoneura fumiferana (CfAFP) are analyzed and discussed in context of its antifreeze activity. The protein comprises of three well-defined planes and one of them binds to the surface of ice. The dynamical properties of solvation water around each of these planes were analyzed separately; the results are compared with the dynamical properties...
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Expression of goose parvovirus whole VP3 protein and its epitopes in Escherichia coli cells
PublicationThe aim of this study was the expression of goose parvovirus capsid protein (VP3) and its epitopes in Escherichia coli cells. Expression of the whole VP3 protein provided an insufficient amount of protein. In contrast, the expression of two VP3 epitopes (VP3ep4, VP3ep6) in E. coli, resulted in very high expression levels. This may suggest that smaller parts of the GPV antigenic determinants are more efficiently expressed than the...
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Integration of protein tethering in a rapid and label-free SERS screening platform for drugs of abuse
PublicationSurface enhanced Raman spectroscopy (SERS) has emerged as a promising technique for the rapid and ultrasensitive detection of molecular species such as drugs of abuse in biofluids. Yet, it remains a significant challenge to create a viable screening tool for multiple drug classes, owing to the lack of affinity of certain species for the SERS substrate and to the matrix interference in complex media. Here we report a protein tethering...
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Novel thermostable single-stranded DNA-binding protein (SSB) from Deinococcus geothermalis
PublicationW celu zbadania właściwości biochemicznych białka wiążącego się do jednoniciowego DNA (SSB) pochodzącego z Deinococcus geothermalis (DgeSSB), sklonowano gen ssb otrzymany w reakcji PCR, a następnie uzyskano wydajną biosyntezę białka DgeSSB. Gen składa się z 900 par zasad, kodujących białko złożone z 300 reszt aminokwasowych, o wyliczonej masie molekularnej równej 32.45 kDa. Sekwencja aminokwasowa wykazuje 43, 44% i 75% identyczności...
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Adipocyte Fatty Acid‐Binding Protein as a Novel Marker of Psoriasis and Clinical Response to Acitretin
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Novel Drying Methods for Sustainable Upcycling of Brewers’ Spent Grains as a Plant Protein Source
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The effect of topical treatment and psoriasis severity on serum retinol-binding protein-4 levels
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Characterization of Structural and Energetic Differences between Conformations of the SARS-CoV-2 Spike Protein
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Expression profiles and genomic organisation of group A protein phosphatase 2C genes inBrassica oleracea
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An analysis and evaluation of the WeFold collaborative for protein structure prediction and its pipelines in CASP11 and CASP12
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Comparison of protein precipitation methods for various rat brain structures prior to proteomic analysis
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Similarities and Differences in the Protein Composition of Cutaneous Melanoma Cells and Their Exosomes Identified by Mass Spectrometry
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The plasma concentration of advanced oxidation protein products and arterial stiffness in apparently healthy adults
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Novel single-stranded DNA-binding protein from psyvhrophilic bacterium Psychrobacter arcticus
PublicationTo study the biochemical properties of SSB from Psychrobacter arcticus (ParSSB), we have cloned the ssb genes obtained by PCR and have developed Escherichia coli overexpression systems. The gene consists of an open reading frame of 642 nucleotides encoding SSB protein of 213 amino acids with a calculated molecular mass of 22.8 kDa. The amino-acid sequence of ParSSB exhibits 49% identity and 57% similarity to Escherichia coli SSB....
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MIC1-MAG1-SAG1 chimeric protein, a most effective antigen for detection of human toxoplasmosis
PublicationThis study describes a Toxoplasma gondii IgG ELISA test based on a new chimeric antigen containing three immunodominant regions from MIC1, MAG1 and SAG1 proteins of a parasite and shows that this test is useful for diagnostic purposes and may replace the lysed and whole-cell antigens.
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Molecular basis of the osmolyte effect on protein stability: a lesson from the mechanical unfolding of lysozyme
PublicationOsmolytes are a class of small organic molecules that shift the protein folding equilibrium. For this reason, they are accumulated by organisms under environmental stress, and find applications in biotechnology where proteins need to be stabilized or dissolved. However, despite years of research, debate continues over the exact mechanisms underpinning the stabilizing and denaturing effect of osmolytes. Here, we simulated the mechanical...
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Blood plasma protein and lipid profile changes in calves during the first week of life
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A Data Driven Model for Predicting RNA-Protein Interactions based on Gradient Boosting Machine
PublicationRNA protein interactions (RPI) play a pivotal role in the regulation of various biological processes. Experimental validation of RPI has been time-consuming, paving the way for computational prediction methods. The major limiting factor of these methods has been the accuracy and confidence of the predictions, and our in-house experiments show that they fail to accurately predict RPI involving short RNA sequences such as TERRA RNA....
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The Role of Electrostatics in Enzymes: Do Biomolecular Force Fields Reflect Protein Electric Fields?
PublicationPreorganization of large, directionally oriented, electric fields inside protein active sites has been proposed as a crucial contributor to catalytic mechanism in many enzymes, and it may be efficiently investigated at the atomistic level with molecular dynamics simulations. Here, we evaluate the ability of the AMOEBA polarizable force field, as well as the additive Amber ff14SB and Charmm C36m models, to describe the electric...
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A highly thermostable, homodimeric single-stranded DNA-binding protein from Deinococcus radiopugnans
PublicationWe report the identification and characterization of the single-stranded DNA-binding protein (SSB) from the mesophile and highly radiation-resistant Deinococcus radiopugnans (DrpSSB). PCR-derived DNA fragment containing the complete structural gene for DrpSSB protein was cloned and expressed in Escherichia coli. The gene consisting of an open reading frame of 900 nucleotides encodes a protein of 300 amino acids with a calculated...
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Aqueous solutions of NMA, Na2HPO4 , and NaH2PO4 as models for interaction studies in phosphate–protein systems
PublicationPhosphate buffers are essential for many areas of studies. However, their influence on buffered systems is often ignored. The phosphate salts can interact with biologically important macromolecules (e.g. proteins) and stabilize or destabilize them. With our research, we want to answer question what kind of interactions, if any, occur between phosphate ions and a protein backbone model — N-methylacetamide (NMA). ATR-FTIR spectroscopy...
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Organic solvents aggregating and shaping structural folding of protein, a case study of the protease enzyme
PublicationLow solubility of reactants or products in aqueous solutions can result in the enzymatic catalytic reactions that can occur in non-aqueous solutions. In current study we investigated aqueous solutions containing different organic solvents / deep eutectic solvents (DESs) that can influence the protease enzyme's activity, structural, and thermal stabilities. Retroviral aspartic protease enzyme is responsible for the cleavage of the...
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Inhibition of amyloid fibril formation of hen egg white lysozyme by trimethylamine N-oxide at low pH
PublicationIn vitro inhibition of the formation of fibrous aggregates of proteins (amyloids) has gained increasing attention due to the number of diseases associated with protein misfolding and fibrillation. An interesting group of compounds for which pronounced activity against this phenomenon can be expected consists of low molecular weight substances (osmolytes) which have the ability to change protein stability. Here we investigate the...
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Standing Waves and Acoustic Heating (or Cooling) in Resonators Filled with Chemically Reacting Gas
PublicationStanding waves and acoustic heating in a one-dimensional resonator filled with chemically reacting gas, is the subject of investigation. The chemical reaction of A ! B type, which takes place in a gas, may be reversible or not. Governing equations for the sound and entropy mode which is generated in the field of sound are derived by use of a special mathematical method. Under some conditions, sound waves propagating in opposite...
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Isothiocyanates may chemically detoxify mutagenic amines formed in heat processed meat
PublicationMeat consumption represents a dietary risk factor increasing the incidence of common cancers, probably due to carcinogenic amines (HAAs) formed upon meat heating. Interestingly, cancers whose incidence is increased by meat consumption, are decreased in populations consuming brassica vegetables regularly. This inverse correlation is attributed to brassica anticarcinogenic components, especially isothiocyanates (ITCs) that stimulate...
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The Effect of Welding Conditions on Mechanical Properties of Superduplex Stainless Steel Welded Joints
PublicationThe tests results of superduplex stainless steel welded joints made with a different heat input, using automatic submerged arc welding (SAW) and semi-automatic flux-cored arc welding (FCAW) have been presented. Metallographic examinations, the measurements of the ferrite content, the width of the heat affected zone (HAZ) and the hardness of the welds in characteristic areas have been performed. Significant differences in the amount of...
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Corrosion behavior of hydrogen charged super duplex stainless steel welded joints
PublicationThe electrochemical behavior of the weld metal, heat-affected zone (HAZ), and base material of super duplex stainless steel (SDSS) welded joints, made with the application of flux-cored arc welding (FCAW) and submerged arc welding (SAW), were investigated with the use of metallographic examinations (optical microscopy and scanning electron microscopy), potentiodynamic polarization measurements and total hydrogen content determination...
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Analysis of features of stainless steels in dissimilar welded joints in chloride inducted corrosion
PublicationStainless steels of femtic-austenitic microstructure that means the duplex Cr-Ni-Mo steels, in comparison with austenitic steel includes less expensive nickel and has much better mechanical properties with good formability and corrosion resistance, even in environments containing chloride ions. Similar share of high chromium ferrite and austenite, which is characterized by high ductility, determines that the duplex steels have...
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Failure of cold-formed beam: How does residual stress affect stability?
PublicationIn machine industry, stresses are often calculated using simple linear FEM analysis. Occasional failures of elements designed in such a way require recomputation by means of more sophisticated methods, eg. including plasticity and non-linear effects. It usually leads to investigation of failure causes and improvement of an element in order to prevent its unwanted behavior in the future. The study presents the case where both linear...
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Left-handed propagation characteristics of a dielectric and metal-loaded periodic circular waveguide
PublicationIn this paper, a periodic dielectric/metallic rod is located in a circular waveguide to obtain left-handed operation. Two geometries of the dielectric/metallic rod are proposed and examined. The dispersion characteristics of the investigated waveguides are obtained using a surface impedance model. Moreover, equivalent circuit models are proposed allowing for calculation of the dispersion characteristics and scattering parameters...
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Synthesis and application of doxorubicin-loaded silica gels as solid materials for spectral analysis
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Synthesis and in vitro characterization of freeze-dried doxorubicin-loaded silica/PEG composite
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Effect of porosity on physical properties of lightweight cement composite with foamed glass aggregate
PublicationThis paper reports on a study of physical properties of lightweight cement composite. We investigate the possibility of replacing traditional aggregate with Granulated Ash Aggregate (GAA) and above all with Granulated Expanded Glass Aggregate (GEGA). For this purpose, 15 specimens of different percentage share of each aggregate in total aggregate volume were tested: 0%, 25%, 50%, 75% or 100% of foam glass aggregate (GEGA) partially...
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Structural and mechanical properties of hydroxyapatite coatings formed by ion-beam assisted deposition
PublicationThe ion-beam assisted deposition (IBAD) is an advanced method capable of producing crystalline coatings at low temperatures. We determined the characteristics of hydroxyapatite Ca10(PO4)6(OH)2 target and coatings formed by IBAD using X-ray photoemission spectroscopy (XPS), X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM) and energy dispersive X-ray (EDX). The composition of the coatings'...
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Cold Cracking Of Underwater Wet Welded S355G10+N High Strength Steel
PublicationWater as the welding environment determines some essential problems influencing steel weldability. Underwater welding of high strength steel joints causes increase susceptibility to cold cracking, which is an effect of much faster heat transfer from the weld area and presence of diffusible hydrogen causing increased metal fragility. The paper evaluates the susceptibility to cold cracking of the high strength S355G10+N steel used,...
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Homoclinic orbits for an almost periodically forced singular Newtonian system in R^3
Publication. This work uses a variational approach to establish the existence of at least two homoclinic solutions for a family of singular Newtonian systems in R^3 which are subjected to almost periodic forcing in time variable
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Experimental investigation of forced convection of water-Al2O3 nanofluids inside horizontal tubes,
PublicationIn this paper, forced convection of water–Al2O3 nanofluids inside horizontal copper tube is studied experimentally. Experiments were conducted for three, i.e. 0.1%, 1% and 5% nanoparticle mass concentrations under transition and turbulent flow regimes. Average heat transfer coefficients and pressure drop values were determined and compared to distilled water. Enhancement of heat transfer for lower nanoparticle concentration and...
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Optical properties of a dielectric slab front-loaded with a grating of plasmonic silver nanowires
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Scaffolds Loaded with Dialdehyde Chitosan and Collagen—Their Physico-Chemical Properties and Biological Assessment
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Experimental Study of the Rolling Friction Coefficient in Highly Loaded Supports of Rotary Kilns
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Processing of polymer‐derived, aerogel‐filled, SiC foams for high‐temperature insulation
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Bulk synthesis of carbon-filled silicon carbide nanotubes with a narrow diameter distribution
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Silver filled single-wall carbon nanotubes—synthesis, structural and electronic properties
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Influence of geometric imperfections on capacities of silo structures loaded with pressure below atmospheric
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Mechanical and Physicochemical Properties of Newly Formed ZnO-PMMA Nanocomposites for Denture Bases
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Influence of geometric imperfections on capacities of silo structures loaded with pressure below atmospheric
PublicationPrzedstawiono probabilistyczną analizę nośności aluminiowego silosu ze wstępnymi imperfekcjami geometrycznymi obciążonego podciśnieniem. Imperfekcje opisano za pomocą dyskretnych odchyłek przyjętych zgodnie z maksymalnymi niedokładnościami dopuszczonymi przez normy. Ponadto wygenerowano imperfekcje płaszcza silosu, stosując jednorodne i niejednorodne pola losowe. Wykonano numeryczne obliczenia geometrycznie i materiałowo nieliniowe.
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Własności wybranych połączeń zgrzewanych wybuchowo. Properties of selected explosive welded joints.
PublicationBadania przeprowadzone w Katedrze Technologii Materiałów Maszynowych i Spawalnictwa obejmowały określenie własności (głównie wytrzymałościowych) szeregu par zgrzanych metali, zarówno w stanie surowym (po zgrzaniu) jak i w niektórych przypadkach, po obróbce cieplnej lub plastycznej. W niniejszej publikacji omówione zostaną tylko niektóre z nich, te które znaj-dują lub mogą znaleźć praktyczne zastosowania i jednocześnie są niezbyt...